CHCHD7 Human

What is the genomic structure and chromosomal location of human CHCHD7?

CHCHD7 in humans, similar to its counterparts in other mammals, contains six exons and is located in close proximity to the PLAG1 gene. In goats, this gene is situated on chromosome 14, with the two genes (CHCHD7 and PLAG1) being transcribed in opposite directions and separated by only 440 bp . The human CHCHD7 gene is situated within a growth-related major quantitative trait locus (QTL) region. This genomic organization is considered highly conserved across different mammalian species, with homology analyses showing significant sequence similarity between cattle, sheep, and goats (for instance, goat CHCHD7 shares 67.76% homology with cattle and 72.50% with sheep CHCHD7) .

Methodologically, researchers interested in the genomic structure can utilize multiple sequence alignment tools such as DNAMAN or MEGA-X to analyze the conservation patterns across species. The NCBI database provides reference sequences that can be compared through calculating nucleotide sequence similarities by counting specific base compositions (A, T, G, C) .

What protein domains characterize CHCHD7 and how do they relate to function?

CHCHD7 protein contains a distinctive and conserved twin CX9C structural motif that is critical to its function . This structural feature is characteristic of the CHCHD7 protein family. The full-length human CHCHD7 protein consists of 97 amino acids, as verified in recombinant expression systems . Sequence analysis of the protein across multiple species reveals a highly conserved common motif across different transcripts, suggesting functional importance in protein interactions .

For researchers investigating protein structure-function relationships, approaches such as recombinant protein expression in systems like Escherichia coli can provide purified protein (>90% purity) suitable for structural and biochemical analyses . The amino acid sequence of human CHCHD7 (MGSSHHHHHHSSGLVPRGSHM GSMHQTRTGKKTVRMPS VTQRLRDPDINPCLSESDASTRCLDENNYDRERCSTYFLRYK NCRRFWNSIVMQRRKNGVKPFMPTAAERDEILRAVGNMPY) can be studied through techniques such as SDS-PAGE and mass spectrometry to determine structural properties .

How does CHCHD7 participate in mitochondrial function?

CHCHD7, also known as COX23 (cytochrome C oxidase assembly homolog), functions as an essential conserved factor for the assembly of cytochrome C oxidase present in the mitochondrial membrane space . The protein plays a critical role in mitochondrial copper homeostasis, which is vital for proper cellular energy production.

Methodologically, researchers investigating CHCHD7's mitochondrial function often employ mitochondrial isolation techniques followed by functional assays for cytochrome C oxidase activity. Studies in model organisms suggest that CHCHD7 may be potentially involved in copper (Cu) delivery during cytochrome C oxidase biosynthesis, maintaining copper homeostasis, or facilitating Cox1 heme transfer during heme assembly . These functions position CHCHD7 as an important regulator of mitochondrial energy production.

When designing experiments to study CHCHD7's mitochondrial function, researchers should consider employing techniques such as blue native polyacrylamide gel electrophoresis to analyze intact mitochondrial protein complexes, or mitochondrial respiration assays to measure the functional consequences of CHCHD7 manipulation.

What is the relationship between CHCHD7 and cellular growth pathways?

CHCHD7 appears to influence growth and developmental pathways through several mechanisms. First, it is located in a major growth-related quantitative trait nucleotide (QTN) region, positioned only 440 bp away from the PLAG1 gene . The PLAG1-CHCHD7 intergenic region contains a major pleiotropic quantitative trait locus (QTL) affecting growth and development traits in various animals, with functional variants identified in the bidirectional promoters of these two genes .

Second, CHCHD7 participates in bone cell metabolism indirectly through its role in regulating cytochrome C oxidase, which is a typical copper-containing enzyme involved in bone metabolism . This connection suggests that CHCHD7 may influence skeletal development and growth.

For researchers studying these pathways, approaches such as gene expression profiling following CHCHD7 knockdown or overexpression can help elucidate downstream effects. Reporter assays utilizing the bidirectional promoter region shared with PLAG1 could provide insights into transcriptional regulation mechanisms affecting growth pathways.

What types of genetic variations have been identified in CHCHD7 and what are their functional impacts?

Several significant genetic variations have been identified in CHCHD7 across species. In goats, a 17-bp insertion/deletion (indel) polymorphism (rs668420586) located 3756 bp downstream of the CHCHD7 gene (specifically described as NC_030821.1:g58695432-58695448delCTTGACAGACACATCCT) has been associated with significant effects on body morphometric traits . This suggests that genetic variations in CHCHD7, even those outside coding regions, may have functional consequences for growth and development.

Genome-wide analyses have revealed that CHCHD7 gene polymorphisms affect growth traits such as body height, body size, and muscle formation in multiple species including cattle, pigs, and humans . These findings indicate a conserved role for CHCHD7 in growth regulation across mammals.

For researchers interested in identifying novel CHCHD7 variants, several methodological approaches are available:

• Direct sequencing

• Agarose gel electrophoresis with sequencing

• PCR-RFLP (Restriction Fragment Length Polymorphism)

• Mathematical Expectation (ME) method for efficient detection of low-frequency variants

The choice of method depends on the estimated mutation frequency. For variants with very low frequency, the ME method offers significantly improved efficiency compared to traditional one-by-one detection methods (36.78% more efficient in SBWC goats and 27.59% in IMWC goats in previous studies) .

How can researchers effectively design studies to evaluate CHCHD7 genetic variants in human populations?

When designing genetic association studies for CHCHD7 variants in humans, researchers should consider several methodological approaches:

How does CHCHD7 interact with PLAG1 and what are the functional consequences of this interaction?

CHCHD7 and PLAG1 have a unique genomic arrangement where they are separated by only 440 bp and transcribed in opposite directions . This arrangement creates a bidirectional promoter configuration that has functional significance. PLAG1 is a fusion partner of CHCHD7, and studies have demonstrated that this interaction affects growth and reproduction in various species .

The functional relationship between these genes is evidenced by studies showing that knockout of PLAG1 in mice results in growth retardation, dwarfism, and impaired spermatogenesis . Additionally, PLAG1 regulates insulin-like growth factor 2 (IGF2) in dogs and humans .

For researchers investigating this interaction, several methodological approaches could be valuable:

• Chromatin immunoprecipitation (ChIP) to study shared regulatory elements between CHCHD7 and PLAG1

• Chromosome conformation capture techniques to evaluate physical interactions between these genomic regions

• Dual luciferase reporter assays to study the bidirectional promoter activity

• Co-immunoprecipitation studies to detect protein-protein interactions

Understanding the regulatory relationship between CHCHD7 and PLAG1 could provide insights into growth disorders and potentially lead to novel therapeutic targets.

What role might CHCHD7 play in human disease pathogenesis?

While specific disease associations for CHCHD7 in humans are still being elucidated, its function in mitochondrial processes suggests potential involvement in disorders characterized by mitochondrial dysfunction. The protein's role in cytochrome C oxidase assembly and copper homeostasis positions it as a candidate gene for conditions involving energy metabolism disorders.

Given CHCHD7's association with growth traits in multiple species, it may also contribute to human growth disorders. Genome-wide analyses have already linked CHCHD7 gene polymorphisms to body height in humans , suggesting potential involvement in growth-related pathologies.

For researchers investigating CHCHD7 in disease contexts, approaches might include:

• Case-control genetic association studies focusing on variants within and around CHCHD7

• Functional assays in patient-derived cells to assess mitochondrial function

• Animal models with CHCHD7 mutations to characterize phenotypic consequences

• Gene expression studies in affected tissues from patients with relevant disorders

What are the optimal methods for detecting and characterizing CHCHD7 genetic variants?

Researchers investigating CHCHD7 genetic variants can employ several complementary approaches:

• Direct sequencing: This provides comprehensive detection of all potential variants but can be resource-intensive for large sample sizes .

• Agarose gel electrophoresis with sequencing: Useful for detecting insertion/deletion polymorphisms with size differences of ≥6 bp. PCR conditions might include touch-down PCR cycling for optimal results .

• PCR-RFLP: Effective for known variants that create or destroy restriction enzyme recognition sites .

• Mathematical Expectation (ME) method: Particularly valuable for detecting variants with low mutation frequency. This approach can significantly improve efficiency compared to traditional one-by-one detection:

  Table 1: Efficiency Comparison of ME Method vs. Traditional Detection

  Population	Sample Size	Ideal Group Size	Predicted Reaction Times	Actual Reaction Times	Efficiency Improvement
  SBWC Goats	1055	11	207	667	36.78%
  IMWC Goats	748	11	146	538	27.59%

  The formula for optimizing the ME method is:
  n = ln(1-(N/a))/ln(1-p)

  Where n is reaction times, N is total sample size, a is sample size per group, and p is estimated mutation frequency .

• Transcription factor binding site prediction: For variants in regulatory regions, tools like Genomatix MatInspector can predict potential effects on transcription factor binding .

How can researchers effectively study CHCHD7 protein function in vitro?

For researchers investigating CHCHD7 protein function, several methodological approaches are recommended:

• Recombinant protein expression: Human CHCHD7 can be successfully expressed in systems such as Escherichia coli, yielding purified protein (>90% purity) suitable for functional and structural studies . The full-length human protein (97 amino acids) can be analyzed using techniques such as SDS-PAGE and mass spectrometry.

• Mitochondrial localization studies: Given CHCHD7's role in mitochondrial processes, subcellular localization studies using fluorescently tagged CHCHD7 constructs can provide insights into its distribution and dynamics within cells.

• Protein interaction studies: Techniques such as yeast two-hybrid screening, co-immunoprecipitation, or proximity labeling approaches can identify CHCHD7 binding partners, potentially revealing novel functional pathways.

• Functional assays: Assessment of cytochrome C oxidase activity and copper homeostasis in cells with modulated CHCHD7 expression can provide direct evidence of the protein's functional roles.

• Structural biology approaches: Techniques such as X-ray crystallography or cryo-electron microscopy could elucidate the three-dimensional structure of CHCHD7, particularly focusing on the conserved twin CX9C structural motif that is critical to its function .

What are the most promising directions for future CHCHD7 research?

Several promising avenues exist for advancing our understanding of CHCHD7 function and its implications:

• Comparative genomics: Further exploration of the evolutionary conservation of CHCHD7 across species could provide insights into its fundamental biological roles. Current data shows varying degrees of homology between species (67.76% between goat and cattle, 72.50% between goat and sheep) , suggesting both conserved and species-specific functions.

• Population genetics: Comprehensive analysis of CHCHD7 genetic variants across different human populations could reveal selection pressures and potential adaptive functions.

• Functional genomics: CRISPR-Cas9 mediated genome editing to create specific CHCHD7 variants could help establish causal relationships between genetic changes and functional outcomes.

• Translational research: Investigation of CHCHD7 in growth disorders, mitochondrial diseases, or metabolic conditions could identify new therapeutic targets and biomarkers.

• Systems biology: Integration of CHCHD7 into broader cellular networks, particularly focusing on its interactions with PLAG1 and other growth-regulatory pathways, could provide a more comprehensive understanding of its biological roles.

Researchers approaching these questions should consider employing multidisciplinary approaches, combining genetic analyses with functional studies and computational modeling to fully elucidate the complex roles of CHCHD7 in human biology and disease.